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- PDB-1oqs: Crystal Structure of RV4/RV7 Complex -

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Basic information

Entry
Database: PDB / ID: 1oqs
TitleCrystal Structure of RV4/RV7 Complex
Components
  • Phospholipase A2 RV-4
  • Phospholipase A2 RV-7
KeywordsHYDROLASE
Function / homology
Function and homology information


phospholipase A2 inhibitor activity / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / phospholipid binding / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Acidic phospholipase A2 RV-7 / Basic phospholipase A2 RV-4
Similarity search - Component
Biological speciesDaboia russellii siamensis (Siamese Russell's viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPerbandt, M. / Betzel, C.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the heterodimeric neurotoxic complex viperotoxin F (RV-4/RV-7) from the venom of Vipera russelli formosensis at 1.9 A resolution.
Authors: Perbandt, M. / Tsai, I.H. / Fuchs, A. / Banumathi, S. / Rajashankar, K.R. / Georgieva, D. / Kalkura, N. / Singh, T.P. / Genov, N. / Betzel, C.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2 RV-7
B: Phospholipase A2 RV-4
C: Phospholipase A2 RV-7
D: Phospholipase A2 RV-4
E: Phospholipase A2 RV-7
F: Phospholipase A2 RV-4
G: Phospholipase A2 RV-7
H: Phospholipase A2 RV-4


Theoretical massNumber of molelcules
Total (without water)110,0798
Polymers110,0798
Non-polymers00
Water6,431357
1
A: Phospholipase A2 RV-7
B: Phospholipase A2 RV-4


Theoretical massNumber of molelcules
Total (without water)27,5202
Polymers27,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area11710 Å2
MethodPISA
2
C: Phospholipase A2 RV-7
D: Phospholipase A2 RV-4


Theoretical massNumber of molelcules
Total (without water)27,5202
Polymers27,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-19 kcal/mol
Surface area11640 Å2
MethodPISA
3
E: Phospholipase A2 RV-7
F: Phospholipase A2 RV-4


Theoretical massNumber of molelcules
Total (without water)27,5202
Polymers27,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-17 kcal/mol
Surface area11690 Å2
MethodPISA
4
G: Phospholipase A2 RV-7
H: Phospholipase A2 RV-4


Theoretical massNumber of molelcules
Total (without water)27,5202
Polymers27,5202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-19 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.918, 85.125, 78.159
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phospholipase A2 RV-7 / Phosphatidylcholine 2-acylhydrolase / Phospholipase A2 inhibitor


Mass: 13689.107 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: venom / Species: Daboia russellii / Strain: siamensis / References: UniProt: P31100, phospholipase A2
#2: Protein
Phospholipase A2 RV-4 / Phosphatidylcholine 2-acylhydrolase


Mass: 13830.759 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Daboia russellii siamensis (Siamese Russell's viper)
Secretion: venom / Species: Daboia russellii / Strain: siamensis / References: UniProt: Q02471, phospholipase A2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44 %
Crystal grow
*PLUS
Temperature: 289 K / pH: 4.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
250 mMsodium acetate1droppH4.5
37 %MPD1reservoir
41 %PEG40001reservoir
51 mM1reservoirpH4.5CaCl2

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 75576 / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 74210 / % possible obs: 98.1 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.95 Å / % possible obs: 97.9 % / Rmerge(I) obs: 0.281

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Processing

SoftwareName: REFMAC / Version: 5.1.16 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.019 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28409 1338 1.8 %RANDOM
Rwork0.22183 ---
obs0.22293 74210 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.415 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å2-0.34 Å2
2--3.16 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7655 0 0 357 8012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0217802
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.1821.92910463
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4725920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.240.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.025940
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3460.24258
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5370.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.6270.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.6521.54740
X-RAY DIFFRACTIONr_mcangle_it2.38327464
X-RAY DIFFRACTIONr_scbond_it3.96733062
X-RAY DIFFRACTIONr_scangle_it5.4054.52999
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 91
Rwork0.292 5008
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.028
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.469
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.133

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